How to create a Syntenic dotplot?

Question

[Chong Tang]

Hello All,

How to create a syntenic dotplot? I'm confused with the method. I have the beginning coordinate and ending coordinate of the genes. Do I need to use the start coordinate as well as end coordinates? Or do I only need to create the plot using the start coordinate? Thanks in advance.

Answer 1

[Biomonika (Noolean)]

As far as I know, synetic dotplot is just regular dotplot with two sequences that are assumed to be homologous. All you need for dotplot are sequences. Maybe they want you to extract the corresponding genes and do dotplot for each gene separately? What species are you working with? What are you comparing to what?

[Chong Tang]

Hi @Noolean! I'd like to accept your advice as the answer. I have already got what I want to know by your reply.